Whole-genome sequence data of a Salmonella enterica serovar Rissen sequence type 8877 isolated from cracked table egg in Sudan

Salmonella enterica serovar Rissen is an emerging and important Salmonella serovar prevalent in live animals and foods from retail markets worldwide. Here, we describe the whole-genome sequence of Salmonella enterica Serovar Rissen Sequence Type 8877 isolated from a cracked table egg in Sudan. The whole-genome sequencing was obtained using Illumina Miseq platform. The quality of the sequenced read, the De novo assembly, and the sequencing typing was conducted by JEKESA pipeline (https://github.com/stanikae/jekesa). The assembled genome was also uploaded to the Center for Genomic Epidemiology web server to determine acquired antibiotic resistance genes, predict the serovar, and the antigenic profile. The genome of Salmonella enterica serovar Rissen 1-M1 was found to harbor 4,689 protein-coding genes, 96 RNA genes, and 115 pseudogenes, as predicted by NCBI Prokaryotic Genome Annotation Pipeline. This whole genome shotgun project has been deposited at DDBJ/ENA/GenBank under accession JAPSFB000000000.


a b s t r a c t
Salmonella enterica serovar Rissen is an emerging and important Salmonella serovar prevalent in live animals and foods from retail markets worldwide. Here, we describe the wholegenome sequence of Salmonella enterica Serovar Rissen Sequence Type 8877 isolated from a cracked table egg in Sudan. The whole-genome sequencing was obtained using Illumina Miseq platform. The quality of the sequenced read, the De novo assembly, and the sequencing typing was conducted by JEKESA pipeline ( https://github.com/stanikae/jekesa ). The assembled genome was also uploaded to the Center for Genomic Epidemiology web server to determine acquired antibiotic resistance genes, predict the serovar, and the antigenic profile. The genome of Salmonella enterica serovar Rissen 1-M1 was found to harbor 4,689 protein-coding genes, 96 RNA genes, and 115 pseudogenes, as predicted by NCBI Prokaryotic Genome Annotation Pipeline. This whole genome shotgun project has been deposited at DDBJ/ENA/GenBank under accession JAPSFB0 0 0 0 0 0 0 0 0.

Value of the Data
• The whole genome sequence data can be used successfully to evaluate the genetic diversity of Salmonella enterica serovar Rissen . • Bioinformaticians can use the genome data in comparative genome analysis as well as evolution of Salmonella enterica serovar Rissen . • The data may also help to investigate the genomic epidemiology of this pathogen.

Objective
Chicken-derived products, particularly table eggs, are the most common source of salmonellosis, one of the most difficult diseases to control in the poultry production industry. Several outbreaks of salmonellosis have been reported, in which the eggs are the source of human infection; especially in the case of undercooked or raw eggs [ 1 , 2 ]. Table eggs can be contaminated on the outer shell surface and internally by any species or serovars of Salmonella [3] . Here, we present a whole-genome sequence analysis of a newly described sequence type of Salmonella enterica serovar Rissen ST8877 isolated from a cracked table egg obtained from a local market in Khartoum, Sudan. To our knowledge, this is the third detection of Rissen ST8877 [4][5][6] , however, this is the first description of its whole genome. Table 1 shows the genome features of Salmonella enterica serovar Rissen sequence type 8877. The sequencing of isolate 1-M1 yielded 2089,086 raw reads. The high-quality reads (2038,422 reads) were assembled to 55 contigs (the longest contig was 521,231 bp) covering 4875,799 bp, with a GC content of 52.1% and N 50 value of 237,445 bp. The genome of 1-M1 was found to harbor 4689 protein-coding genes, 96 RNA genes, and 115 pseudogenes, as predicted by the NCBI PGAP. MLST based on the Salmonella enterica seven-allele scheme indicated ST8877. Res-Finder detected aminoglycoside resistance gene aac(6 )-Iaa (98.1%, NC_003197) which increases resistance to tobramycin and/or amikacin [7] . Serotyping of 1-M1 resulted in the serovar Rissen and the antigenic profile was identified as O7:H1f.g:H2-(H2 antigen was not identified). PlasmidFinder identified only Col (pHAD28) plasmid replicon sequence (91.6 %, KU674895). Up to 23 SPIs were detected in these genomes, including SPI-1 (7 islands), SPI-2 (8 islands), SPI-3 (2 islands), SPI-4 (1 island), SPI-5 (1 island), SPI-8 (1 island), SPI-9 (1 island), C63PI (1 islands), and CS54 (1 island). The Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JAPSFB0 0 0 0 0 0 0 0 0. The version described in this report is version JAPSFB010 0 0 0 0 0 0.

Experimental Design, Materials and Methods
In 2019, a cracked egg (produced by a white Leghorn commercial laying chicken) was collected from a retail shop in a local market in Khartoum city in Sudan. The egg was collected under aseptic conditions and analyzed immediately within 2 hours using previously described methods for isolation and identification [8] . The egg content was mixed thoroughly before taking a sample for bacteriology. A sterile swab was soaked in normal saline and then applied to the surface of the egg. The swab was then dipped into a test tube containing 10 ml normal saline and the contents were mixed thoroughly using a vortex mixer. Serial dilutions up to 10 5 were then prepared. One ml was taken from appropriate dilution and inoculated into Xylose-Lysine Deoxycholate agar (M031, HiMedia, India), a proper selective medium for the isolation of Salmonella [9] . The culture was incubated at 37 °C for 2-48 h and examined for the presence of typical colonies of Salmonella (red with a black centre). The colonies were further subjected to biochemical testing. The DNA was extracted using the QIAamp DNA minikit (Qiagen, Germany), and paired-end libraries were prepared using the Nextera DNA Flex library kit, followed by 2 × 300 bp sequencing on a MiSeq machine (Illumina, Inc., USA). For wholegenome sequence analysis and typing, the JEKESA pipeline ( https://github.com/stanikae/jekesa ) was used. Briefly, Trim Galore v0.6.2 ( https://github.com/FelixKrueger/TrimGalore ) was used to filter the sequence reads (Q, ≥ 20; length, ≥ 50), de novo assembly was performed using SPAdes v3.13.2 ( https://github.com/ablab/spades ),the assemblies were polished and optimized using Shovill v1.1.0 ( https://github.com/tseemann/shovill ), and sequence typing was done using the multilocus sequence typing (MLST) tool v2.16.4 ( https://github.com/tseemann/mlst ). Assembly metrics, including the GC content and number of contigs, were calculated using QUAST v5.0.2 ( http://quast.sourceforge.net/quast ). All resultant contiguous sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline v4.13 [10] . Furthermore, the assembled genome was uploaded to the Center for Genomic Epidemiology web server; to determine acquired an-tibiotic resistance genes using ResFinder v4.1 [11][12][13] ; to predict the serovar and the antigenic profile (O, H1 and H2 antigens) using SeqSero v1.2 [14] , to identify plasmids using PlasmidFinder v2.1 [ 13 , 15 ], and to determine salmonella pathogenicity islands using SPIFinder v2.0 [16] .

Ethics Statements
This work did not involve studies with animals or humans.

Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.